# List of top-scoring protein chains for t2k-w0.5 hidden Markov model. # HMM and HMM E-value scores computed by SAM (c) 1992-2001 Regents of the University of California, Santa Cruz # Sequence Alignment and Modeling Software System # http://www.cse.ucsc.edu/research/compbio/sam.html # ----------------- Citations (SAM, SAM-T99, HMMs) -------------------- # R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: # Extension and analysis of the basic method, CABIOS 12:95-107, 1996. # K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting # remote protein homologies, Bioinformatics 14(10):846-856, 1998. # A. Krogh et al., Hidden Markov models in computational biology: # Applications to protein modeling, JMB 235:1501-1531, Feb 1994. # # FSSP representative for each protein chain taken from FSSP: # ------------------Citations (FSSP) ----------------------------------- # L. Holm and C. Sander (1996) Mapping the protein universe. Science 273:595-602. # #SCOP domains found in each protein chain taken from SCOP: # ------------------Citations (SCOP) ----------------------------------- #Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995). #SCOP: a structural classification of proteins database for the investigation of sequences and structures. #J. Mol. Biol. 247, 536-540. Sequence_ID Length Target_Evalue FSSP-rep SCOP_domain SCOP_suid 5S 5N 12S 6S 12S 10N 1dciA 275 1.18e-01 1dciA c.14.1.3 30918 1mioB 458 5.88e-01 1qguB c.92.2.3 35602 1bvuA 418 6.02e-01 1hwyA c.2.1.7 30226 c.58.1.1 33874 1hzdA 272 6.91e-01 c.14.1.3 65969 1ef8A 261 1.03e+00 1ef8A c.14.1.3 30921 1euzE 419 1.60e+00 1k89 c.2.1.7 59521 c.58.1.1 59522 1ii7A 333 1.79e+00 1ii7A d.159.1.4 62415 1kk1A 410 2.05e+00 1kk3A 410 2.12e+00 1htlA 191 3.06e+00 1lt3A d.166.1.1 42237 2dubE 261 3.18e+00 1nzyA c.14.1.3 30916 1kk0A 410 3.19e+00 1ey3A 258 3.21e+00 c.14.1.3 64911 1ltiA 192 4.23e+00 1lt3A d.166.1.1 42233 1ltgA 191 4.28e+00 1lt3A d.166.1.1 42235 1gtmA 419 4.33e+00 1hwyA c.2.1.7 30223 c.58.1.1 33871 1hnuA 280 4.56e+00 1hnoA c.14.1.3 61096 1hnoA 280 4.56e+00 1hnoA c.14.1.3 61095 1ltsA 185 4.65e+00 1lt3A d.166.1.1 42229 1ltaA 188 4.76e+00 1lt3A d.166.1.1 42232 1dosA 358 4.84e+00 1dosA c.1.10.2 29175 1b57A 358 5.38e+00 1dosA c.1.10.2 29177 1llc 325 5.47e+00 1hyhA c.2.1.5 30176 d.162.1.1 42143 1lt3A 240 6.26e+00 1lt3A d.166.1.1 42230 1lt4A 247 6.37e+00 1lt3A d.166.1.1 42231 1d2eA 397 7.03e+00 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1j9yA 385 7.07e+00 1j9yA c.1.8.3 62791 1etu 394 8.16e+00 1efcA c.37.1.8 64737 1efm 393 8.22e+00 1efcA c.37.1.8 64732 1ksiA 642 8.38e+00 1ksiB b.30.2.1 24408 d.17.2.1 38043 d.17.2.1 38044 1ksiB 642 8.38e+00 1ksiB b.30.2.1 24409 d.17.2.1 38045 d.17.2.1 38046 1cfzA 162 8.78e+00 1cfzA c.56.1.1 33754 1ebdA 455 9.17e+00 1lvl c.3.1.5 30577 c.3.1.5 30578 d.87.1.1 40210 1av4 638 9.26e+00 1a2vA b.30.2.1 24411 d.17.2.1 38049 d.17.2.1 38050 1qdeA 224 9.44e+00 1qvaA c.37.1.13 32410 1d8tA 393 9.69e+00 1efcA b.43.3.1 25686 b.44.1.1 25726 c.37.1.8 32119 1dg1G 394 9.72e+00 1efcA b.43.3.1 25684 b.44.1.1 25724 c.37.1.8 32117 1efuA 385 9.72e+00 1efcA b.43.3.1 25682 b.44.1.1 25722 c.37.1.8 32115 1efcA 393 9.72e+00 1efcA b.43.3.1 25680 b.44.1.1 25720 c.37.1.8 32113 1hq0A 295 9.95e+00 1hzgA d.194.1.1 61122 1avk 638 1.00e+01 1a2vA b.30.2.1 24410 d.17.2.1 38047 d.17.2.1 38048 1jx2B 315 1.09e+01 c.37.1.8 67404 1qvaA 223 1.09e+01 1qvaA c.37.1.13 32411 1eft 405 1.12e+01 1efcA b.43.3.1 25688 b.44.1.1 25728 c.37.1.8 32123 1g7tA 594 1.13e+01 1g7rA b.43.3.1 25714 b.43.3.1 25715 c.20.1.1 31033 c.37.1.8 32148 1g7sA 594 1.13e+01 1g7rA b.43.3.1 25712 b.43.3.1 25713 c.20.1.1 31032 c.37.1.8 32147 1hzgA 295 1.13e+01 1hzgA d.194.1.1 61436 1b23P 405 1.16e+01 1efcA b.43.3.1 25689 b.44.1.1 25729 c.37.1.8 32124 1csmA 256 1.18e+01 5csmA a.130.1.2 19495 1dtwA 400 1.23e+01 1qs0A c.36.1.3 31827 1a0dA 440 1.28e+01 1a0cA c.1.15.3 29533 3csmA 256 1.33e+01 5csmA a.130.1.2 19500 5csmA 256 1.35e+01 5csmA a.130.1.2 19494 4csmA 256 1.38e+01 5csmA a.130.1.2 19498 1exmA 405 1.43e+01 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1ha3A 405 1.43e+01 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1d7kA 421 1.43e+01 7odcA b.49.2.1 26486 c.1.6.1 28648 1jdbF 382 1.43e+01 c.8.3.1 30757 c.23.16.1 31434 1c3oB 382 1.45e+01 1c3oB c.8.3.1 30744 c.23.16.1 31421 1k3bA 119 1.46e+01 1aipE 405 1.46e+01 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1a9xB 379 1.49e+01 1c3oB c.8.3.1 30732 c.23.16.1 31409 1cs0B 382 1.58e+01 1c3oB c.8.3.1 30740 c.23.16.1 31417 1eqjA 511 1.61e+01 1ejjA c.105.1.1 59495 c.76.1.3 59496 1ejjA 511 1.61e+01 1ejjA c.105.1.1 59422 c.76.1.3 59423 1ej6A 1289 1.78e+01 i.7.1.1 45967 8pchA 220 1.78e+01 1cs8A d.3.1.1 37084 3lriA 83 1.92e+01 1zeiA g.1.1.1 43995 1g7rA 594 2.03e+01 1g7rA b.43.3.1 25716 b.43.3.1 25717 c.20.1.1 31034 c.37.1.8 32149 1rpxA 230 2.05e+01 1rpxA c.1.2.2 28536 1gbnA 402 2.10e+01 2dkb c.67.1.4 34455 1ntd 343 2.10e+01 1nif b.6.1.3 23088 b.6.1.3 23089 1fieB 731 2.10e+01 1f13A b.1.1.5 21880 b.1.5.1 22169 b.1.5.1 22170 d.3.1.4 37110 2oatA 439 2.13e+01 2dkb c.67.1.4 34452 1oatA 439 2.13e+01 2dkb c.67.1.4 34461 1jjuB 337 2.15e+01 b.69.2.2 66779 1diiA 521 2.17e+01 1qltA d.58.32.1 39481 d.145.1.1 41744 1ibvB 229 2.24e+01 3dbvO 334 2.25e+01 1dssG c.2.1.3 29982 d.81.1.1 39897 1dmuA 299 2.31e+01 1dmuA c.52.1.4 33294 1g47A 77 2.31e+01 1g47A g.39.1.3 45147 g.39.1.3 45148 1bqyA 234 2.35e+01 5ptp b.47.1.2 26332 1csbB 205 2.40e+01 1theB 1cec 343 2.41e+01 1ceo c.1.8.3 28809 1ceo 343 2.41e+01 1ceo c.1.8.3 28808 1bz7B 217 2.44e+01 1igtB b.1.1.1 20403 b.1.1.2 21375 1ekeA 230 2.44e+01 1ekeA c.55.3.1 33572 1evuA 731 2.47e+01 1f13A b.1.1.5 21883 b.1.5.1 22175 b.1.5.1 22176 d.3.1.4 37113 1j9qA 341 2.53e+01 1nif b.6.1.3 62765 b.6.1.3 62766 1f13A 731 2.55e+01 1f13A b.1.1.5 21877 b.1.5.1 22163 b.1.5.1 22164 d.3.1.4 37107 1ggtB 731 2.55e+01 1f13A b.1.1.5 21882 b.1.5.1 22173 b.1.5.1 22174 d.3.1.4 37112 1gguA 731 2.55e+01 1f13A b.1.1.5 21885 b.1.5.1 22179 b.1.5.1 22180 d.3.1.4 37115 1qrkA 731 2.55e+01 1f13A b.1.1.5 21889 b.1.5.1 22187 b.1.5.1 22188 d.3.1.4 37119 1e44A 85 2.56e+01 3eipA d.26.2.1 59219 1pyaB 228 2.56e+01 1pyaB 3eipA 84 2.59e+01 3eipA d.26.2.1 38434 1db0B 331 2.62e+01 1d0nA d.109.1.1 40854 d.109.1.1 40855 d.109.1.1 40856 1lgyA 269 2.78e+01 3tgl c.69.1.17 34758 1xypA 190 2.79e+01 1axkA b.29.1.11 24327 1d0nA 729 2.86e+01 1d0nA d.109.1.1 40834 d.109.1.1 40835 d.109.1.1 40836 d.109.1.1 40837 d.109.1.1 40838 d.109.1.1 40839 1cknA 330 2.96e+01 1ckmA b.40.4.6 25360 d.142.2.3 41587 1ckmA 330 2.96e+01 1ckmA b.40.4.6 25358 d.142.2.3 41585 1cknB 330 2.99e+01 1ckmA b.40.4.6 25361 d.142.2.3 41588 1bn5 478 3.04e+01 1bn5 a.4.5.25 16224 d.127.1.1 41161 1ab4 477 3.05e+01 1ab4 e.11.1.1 43251 1lfpA 249 3.38e+01 1b6a 478 3.46e+01 1bn5 a.4.5.25 16223 d.127.1.1 41160 1egdA 396 3.46e+01 3mdeA a.29.3.1 16596 e.6.1.1 42857 1i4uA 181 3.70e+01 b.60.1.1 61732 1lucB 324 3.81e+01 1lucA c.1.16.1 29548 1brlB 324 3.81e+01 1lucA c.1.16.1 29554 1i4zA 114 3.95e+01 2mhr a.24.4.1 61746 1egeA 396 3.97e+01 3mdeA a.29.3.1 16604 e.6.1.1 42865